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Nazarizadeh M, Nováková M, Drábková M, Catchen J, Olson PD, Štefka J. Highly resolved genome assembly and comparative transcriptome profiling reveal genes related to developmental stages of tapeworm Ligula intestinalis. Proc Biol Sci 2024; 291:20232563. [PMID: 38290545 PMCID: PMC10827431 DOI: 10.1098/rspb.2023.2563] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 01/02/2024] [Indexed: 02/01/2024] Open
Abstract
Ligula intestinalis (Cestoda: Diphyllobothriidae) is an emerging model organism for studies on parasite population biology and host-parasite interactions. However, a well-resolved genome and catalogue of its gene content has not been previously developed. Here, we present the first genome assembly of L. intestinalis, based on Oxford Nanopore Technologies, Illumina and Omni-C sequencing methodologies. We use transcriptome profiling to compare plerocercoid larvae and adult worms and identify differentially expressed genes (DEGs) associated with these life stages. The genome assembly is 775.3 mega (M)bp in size, with scaffold N50 value of 118 Mbp and encodes 27 256 predicted protein-coding sequences. Over 60% of the genome consists of repetitive sequences. Synteny analyses showed that the 10 largest scaffolds representing 75% of the genome display high correspondence to full chromosomes of cyclophyllidean tapeworms. Mapping RNA-seq data to the new reference genome, we identified 3922 differentially expressed genes in adults compared with plerocercoids. Gene ontology analyses revealed over-represented genes involved in reproductive development of the adult stage (e.g. sperm production) and significantly enriched DEGs associated with immune evasion of plerocercoids in their fish host. This study provides the first insights into the molecular biology of L. intestinalis and provides the most highly contiguous assembly to date of a diphyllobothriid tapeworm useful for population and comparative genomic investigations of parasitic flatworms.
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Affiliation(s)
- Masoud Nazarizadeh
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
- Institute of Parasitology, Biology Centre CAS, České Budějovice, Czech Republic
| | - Milena Nováková
- Institute of Parasitology, Biology Centre CAS, České Budějovice, Czech Republic
| | - Marie Drábková
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Julian Catchen
- Department of Evolution, Ecology and Behavior, University of Illinois, Urbana-Champaign, IL 61801, USA
| | - Peter D. Olson
- Life Sciences Department, Natural History Museum, London, UK
| | - Jan Štefka
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
- Institute of Parasitology, Biology Centre CAS, České Budějovice, Czech Republic
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2
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Herz M, Zarowiecki M, Wessels L, Pätzel K, Herrmann R, Braun C, Holroyd N, Huckvale T, Bergmann M, Spiliotis M, Koziol U, Berriman M, Brehm K. Genome-wide transcriptome analysis of Echinococcus multilocularis larvae and germinative cell cultures reveals genes involved in parasite stem cell function. Front Cell Infect Microbiol 2024; 14:1335946. [PMID: 38333034 PMCID: PMC10850878 DOI: 10.3389/fcimb.2024.1335946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 01/12/2024] [Indexed: 02/10/2024] Open
Abstract
The lethal zoonosis alveolar echinococcosis is caused by tumour-like growth of the metacestode stage of the tapeworm Echinococcus multilocularis within host organs. We previously demonstrated that metacestode proliferation is exclusively driven by somatic stem cells (germinative cells), which are the only mitotically active parasite cells that give rise to all differentiated cell types. The Echinococcus gene repertoire required for germinative cell maintenance and differentiation has not been characterised so far. We herein carried out Illumina sequencing on cDNA from Echinococcus metacestode vesicles, from metacestode tissue depleted of germinative cells, and from Echinococcus primary cell cultures. We identified a set of ~1,180 genes associated with germinative cells, which contained numerous known stem cell markers alongside genes involved in replication, cell cycle regulation, mitosis, meiosis, epigenetic modification, and nucleotide metabolism. Interestingly, we also identified 44 stem cell associated transcription factors that are likely involved in regulating germinative cell differentiation and/or pluripotency. By in situ hybridization and pulse-chase experiments, we also found a new general Echinococcus stem cell marker, EmCIP2Ah, and we provide evidence implying the presence of a slow cycling stem cell sub-population expressing the extracellular matrix factor Emkal1. RNA-Seq analyses on primary cell cultures revealed that metacestode-derived Echinococcus stem cells display an expanded differentiation capability and do not only form differentiated cell types of the metacestode, but also cells expressing genes specific for protoscoleces, adult worms, and oncospheres, including an ortholog of the schistosome praziquantel target, EmTRPMPZQ. Finally, we show that primary cell cultures contain a cell population expressing an ortholog of the tumour necrosis factor α receptor family and that mammalian TNFα accelerates the development of metacestode vesicles from germinative cells. Taken together, our analyses provide a robust and comprehensive characterization of the Echinococcus germinative cell transcriptome, demonstrate expanded differentiation capability of metacestode derived stem cells, and underscore the potential of primary germinative cell cultures to investigate developmental processes of the parasite. These data are relevant for studies into the role of Echinococcus stem cells in parasite development and will facilitate the design of anti-parasitic drugs that specifically act on the parasite germinative cell compartment.
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Affiliation(s)
- Michaela Herz
- Consultant Laboratory for Echinococcosis, Institute of Hygiene and Microbiology, University of Würzburg, Würzburg, Germany
| | | | - Leonie Wessels
- Consultant Laboratory for Echinococcosis, Institute of Hygiene and Microbiology, University of Würzburg, Würzburg, Germany
| | - Katharina Pätzel
- Consultant Laboratory for Echinococcosis, Institute of Hygiene and Microbiology, University of Würzburg, Würzburg, Germany
| | - Ruth Herrmann
- Consultant Laboratory for Echinococcosis, Institute of Hygiene and Microbiology, University of Würzburg, Würzburg, Germany
| | - Christiane Braun
- Consultant Laboratory for Echinococcosis, Institute of Hygiene and Microbiology, University of Würzburg, Würzburg, Germany
| | - Nancy Holroyd
- Parasite Genomics, Wellcome Sanger Institute, Cambridge, United Kingdom
| | - Thomas Huckvale
- Parasite Genomics, Wellcome Sanger Institute, Cambridge, United Kingdom
| | - Monika Bergmann
- Consultant Laboratory for Echinococcosis, Institute of Hygiene and Microbiology, University of Würzburg, Würzburg, Germany
| | - Markus Spiliotis
- Consultant Laboratory for Echinococcosis, Institute of Hygiene and Microbiology, University of Würzburg, Würzburg, Germany
| | - Uriel Koziol
- Consultant Laboratory for Echinococcosis, Institute of Hygiene and Microbiology, University of Würzburg, Würzburg, Germany
- Sección Biología Celular, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Matthew Berriman
- Parasite Genomics, Wellcome Sanger Institute, Cambridge, United Kingdom
| | - Klaus Brehm
- Consultant Laboratory for Echinococcosis, Institute of Hygiene and Microbiology, University of Würzburg, Würzburg, Germany
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Grecco A, Macchiaroli N, Pérez MG, Casulli A, Cucher MA, Rosenzvit MC. microRNA silencing in a whole worm cestode model provides insight into miR-71 function. Int J Parasitol 2023; 53:699-710. [PMID: 37699506 DOI: 10.1016/j.ijpara.2023.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 06/13/2023] [Accepted: 08/05/2023] [Indexed: 09/14/2023]
Abstract
Parasites belonging to the class Cestoda include zoonotic species such as Echinococcus spp. and Taenia spp. that cause morbidity and mortality in endemic areas, mainly affecting pastoral and rural communities in low income countries but also upper middle income countries. Cestodes show remarkable developmental plasticity, implying tight regulation of gene expression throughout their complex life cycles. Despite the recent availability of genomic data for cestodes, little progress was made on postgenomic functional studies. MicroRNAs (miRNAs) are key components of gene regulatory systems that guide diverse developmental processes in multicellular organisms. miR-71 is a highly expressed miRNA in cestodes, which is absent in vertebrates and targets essential parasite genes, representing a potential key player in understanding the role of miRNAs in cestodes biology. Here we used transfection with antisense oligonucleotides to perform whole worm miRNA knockdown in tetrathyridia of Mesocestoides vogae (syn. Mesocestoides corti), a laboratory model of cestodes. We believe this is the first report of miRNA knockdown at the organism level in these parasites. Our results showed that M. vogae miR-71 is involved in the control of strobilation in vitro and in the establishment of murine infection. In addition, we identified miR-71 targets in M. vogae, several of them being de-repressed upon miR-71 knockdown. This study provides new knowledge on gene expression regulation in cestodes and suggests that miRNAs could be evaluated as new selective therapeutic targets for treating Neglected Tropical Diseases prioritised by the World Health Organization.
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Affiliation(s)
- Andrés Grecco
- Departamento de Microbiología, Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires, Argentina; Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPaM, UBA-CONICET), Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Natalia Macchiaroli
- Laboratorio de Genómica y Bioinformática de Patógenos, Instituto de Biociencias, Biotecnología y Biología Traslacional (iB3), Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Matías Gastón Pérez
- Departamento de Microbiología, Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires, Argentina; Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPaM, UBA-CONICET), Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Adriano Casulli
- WHO Collaborating Centre for the Epidemiology, Detection and Control of Cystic and Alveolar Echinococcosis. Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy; European Reference Laboratory for Parasites. Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Marcela Alejandra Cucher
- Departamento de Microbiología, Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires, Argentina; Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPaM, UBA-CONICET), Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Mara Cecilia Rosenzvit
- Departamento de Microbiología, Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires, Argentina; Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPaM, UBA-CONICET), Universidad de Buenos Aires, Buenos Aires, Argentina.
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Montagne J, Preza M, Koziol U. Stem cell proliferation and differentiation during larval metamorphosis of the model tapeworm Hymenolepis microstoma. Front Cell Infect Microbiol 2023; 13:1286190. [PMID: 37908761 PMCID: PMC10614006 DOI: 10.3389/fcimb.2023.1286190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 10/02/2023] [Indexed: 11/02/2023] Open
Abstract
Background Tapeworm larvae cause important diseases in humans and domestic animals. During infection, the first larval stage undergoes a metamorphosis where tissues are formed de novo from a population of stem cells called germinative cells. This process is difficult to study for human pathogens, as these larvae are infectious and difficult to obtain in the laboratory. Methods In this work, we analyzed cell proliferation and differentiation during larval metamorphosis in the model tapeworm Hymenolepis microstoma, by in vivo labelling of proliferating cells with the thymidine analogue 5-ethynyl-2'-deoxyuridine (EdU), tracing their differentiation with a suite of specific molecular markers for different cell types. Results Proliferating cells are very abundant and fast-cycling during early metamorphosis: the total number of cells duplicates every ten hours, and the length of G2 is only 75 minutes. New tegumental, muscle and nerve cells differentiate from this pool of proliferating germinative cells, and these processes are very fast, as differentiation markers for neurons and muscle cells appear within 24 hours after exiting the cell cycle, and fusion of new cells to the tegumental syncytium can be detected after only 4 hours. Tegumental and muscle cells appear from early stages of metamorphosis (24 to 48 hours post-infection); in contrast, most markers for differentiating neurons appear later, and the detection of synapsin and neuropeptides correlates with scolex retraction. Finally, we identified populations of proliferating cells that express conserved genes associated with neuronal progenitors and precursors, suggesting the existence of tissue-specific lineages among germinative cells. Discussion These results provide for the first time a comprehensive view of the development of new tissues during tapeworm larval metamorphosis, providing a framework for similar studies in human and veterinary pathogens.
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Affiliation(s)
| | | | - Uriel Koziol
- Sección Biología Celular, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
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Trans-splicing in the cestode Hymenolepis microstoma is constitutive across the life cycle and depends on gene structure and composition. Int J Parasitol 2023; 53:103-117. [PMID: 36621599 DOI: 10.1016/j.ijpara.2022.11.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 10/31/2022] [Accepted: 11/10/2022] [Indexed: 01/07/2023]
Abstract
Spliced leader (SL) trans-splicing is a key process during mRNA maturation of many eukaryotes, in which a short sequence (SL) is transferred from a precursor SL-RNA into the 5' region of an immature mRNA. This mechanism is present in flatworms, in which it is known to participate in the resolution of polycistronic transcripts. However, most trans-spliced transcripts are not part of operons, and it is not clear if this process may participate in additional regulatory mechanisms in this group. In this work, we present a comprehensive analysis of SL trans-splicing in the model cestode Hymenolepis microstoma. We identified four different SL-RNAs which are indiscriminately trans-spliced to 622 gene models. SL trans-splicing is enriched in constitutively expressed genes and does not appear to be regulated throughout the life cycle. Operons represented at least 20% of all detected trans-spliced gene models, showed conservation to those of the cestode Echinococcus multilocularis, and included complex loci such as an alternative operon (processed as either a single gene through cis-splicing or as two genes of a polycistron). Most insertion sites were identified in the 5' untranslated region (UTR) of monocistronic genes. These genes frequently contained introns in the 5' UTR, in which trans-splicing used the same acceptor sites as cis-splicing. These results suggest that, unlike other eukaryotes, trans-splicing is associated with internal intronic promoters in the 5' UTR, resulting in transcripts with strong splicing acceptor sites without competing cis-donor sites, pointing towards a simple mechanism driving the evolution of novel SL insertion sites.
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Phuphisut O, Poodeepiyasawat A, Yoonuan T, Watthanakulpanich D, Chotsiri P, Reamtong O, Mousley A, Gobert GN, Adisakwattana P. Transcriptome profiling of male and female Ascaris lumbricoides reproductive tissues. Parasit Vectors 2022; 15:477. [PMID: 36539906 PMCID: PMC9768952 DOI: 10.1186/s13071-022-05602-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Accepted: 11/30/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Ascaris lumbricoides causes human ascariasis, the most prevalent helminth disease, infecting approximately 1 billion individuals globally. In 2019 the global disease burden was estimated to be 754,000 DALYs and resulted in 2090 deaths. In the absence of a vaccination strategy, treatment of ascariasis has relied on anthelminthic chemotherapy, but drug resistance is a concern. The propensity for reinfection is also a major challenge to disease control; female worms lay up to 200,000 eggs daily, which contaminate surrounding environments and remain viable for years, resulting in high transmission rates. Understanding the molecular mechanisms of reproductive processes, including control of egg production, spermatogenesis, oogenesis and embryogenesis, will drive the development of new drugs and/or vaccine targets for future ascariasis control. METHODS Transcriptome profiles of discrete reproductive and somatic tissue samples were generated from adult male and female worms using Illumina HiSeq with 2 × 150 bp paired-end sequencing. Male tissues included: testis germinal zone, testis part of vas deferens, seminal vesicle and somatic tissue. Female tissues included: ovary germinal zone, ovary part of the oviduct, uterus and somatic tissue. Differentially expressed genes (DEGs) were identified from the fragments per kilobases per million reads (FPKM) profiles. Hierarchical analysis was performed to identify tissue-specific genes. Furthermore, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were employed to identify significant terms and pathways for the DEGs. RESULTS DEGs involved in protein phosphorylation and adhesion molecules were indicated to play a crucial role in spermatogenesis and fertilization, respectively. Those genes associated with the G-protein-coupled receptor (GPCR) signaling pathway and small GTPase-mediated signal transduction pathway play an essential role in cytoskeleton organization during oogenesis. Additionally, DEGs associated with the SMA genes and TGF-β signaling pathway are crucial in adult female embryogenesis. Some genes associated with particular biological processes and pathways that were identified in this study have been linked to defects in germline development, embryogenesis and reproductive behavior. In the enriched KEGG pathway analysis, Hippo signaling, oxytocin signaling and tight junction pathways were identified to play a role in Ascaris male and female reproductive systems. CONCLUSIONS This study has provided comprehensive transcriptome profiles of discrete A. lumbricoides reproductive tissue samples, revealing the molecular basis of these functionally important tissues. The data generated from this study will provide fundamental knowledge on the reproductive biology of Ascaris and will inform future target identification for anti-ascariasis drugs and/or vaccines.
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Affiliation(s)
- Orawan Phuphisut
- Department of Helminthology, Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400, Thailand
| | - Akkarin Poodeepiyasawat
- Department of Helminthology, Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400, Thailand
| | - Tippayarat Yoonuan
- Department of Helminthology, Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400, Thailand
| | - Dorn Watthanakulpanich
- Department of Helminthology, Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400, Thailand
| | - Palang Chotsiri
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, 10400, Thailand
| | - Onrapak Reamtong
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400, Thailand
| | - Angela Mousley
- School of Biological Sciences, Queen's University Belfast, Belfast, BT9 5DL, UK
| | - Geoffrey N Gobert
- School of Biological Sciences, Queen's University Belfast, Belfast, BT9 5DL, UK
| | - Poom Adisakwattana
- Department of Helminthology, Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400, Thailand.
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Preza M, Van Bael S, Temmerman L, Guarnaschelli I, Castillo E, Koziol U. Global analysis of neuropeptides in cestodes identifies Attachin, a SIFamide homolog, as a stimulant of parasite motility and attachment. J Neurochem 2022; 162:467-482. [PMID: 35689626 DOI: 10.1111/jnc.15654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 06/07/2022] [Accepted: 06/08/2022] [Indexed: 11/28/2022]
Abstract
Many anthelmintics target the neuromuscular system, in particular by interfering with signaling mediated by classical neurotransmitters. Although peptidergic signaling has been proposed as a novel target for anthelmintics, current knowledge of the neuropeptide complement of many helminth groups is still limited, especially for parasitic flatworms (cestodes, trematodes, and monogeneans). In this work, we have characterized the neuropeptide complement of the model cestode Hymenolepis microstoma. Peptidomic characterization of adults of H. microstoma validated many of the neuropeptide precursor (npp) genes previously predicted in silico, and identified novel neuropeptides that are conserved in parasitic flatworms. Most neuropeptides from parasitic flatworms lack significant similarity to those from other animals, confirming the uniqueness of their peptidergic signaling. Analysis of gene expression of ten npp genes by in situ hybridization confirmed that all of them are expressed in the nervous system and identified cryptic features, including the first evidence of dorsoventral asymmetry, as well as a new population of peripheral peptidergic cells that appears to be conserved in the trematode Schistosoma mansoni. Finally, we characterized in greater detail Attachin, an SIFamide homolog. Although its expression is largely restricted to the longitudinal nerve cords and cerebral commissure in H. microstoma, it shows widespread localization in the larval nervous system of Echinococcus multilocularis and Mesocestoides corti. Exogenous addition of a peptide corresponding to the highly conserved C-terminus of Attachin stimulated motility and attachment of M. corti larvae. Altogether, this work provides a robust experimental foothold for the characterization of peptidergic signaling in parasitic flatworms.
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Affiliation(s)
- Matías Preza
- Sección Biología Celular, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Sven Van Bael
- Animal Physiology and Neurobiology, University of Leuven (KU Leuven), Leuven, Belgium
| | - Liesbet Temmerman
- Animal Physiology and Neurobiology, University of Leuven (KU Leuven), Leuven, Belgium
| | - Inés Guarnaschelli
- Sección Biología Celular, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Estela Castillo
- Laboratorio de Biología Parasitaria, Instituto de Higiene, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Uriel Koziol
- Sección Biología Celular, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
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Munck S, Cawthorne C, Escamilla‐Ayala A, Kerstens A, Gabarre S, Wesencraft K, Battistella E, Craig R, Reynaud EG, Swoger J, McConnell G. Challenges and advances in optical 3D mesoscale imaging. J Microsc 2022; 286:201-219. [PMID: 35460574 PMCID: PMC9325079 DOI: 10.1111/jmi.13109] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 03/02/2022] [Accepted: 04/14/2022] [Indexed: 12/14/2022]
Abstract
Optical mesoscale imaging is a rapidly developing field that allows the visualisation of larger samples than is possible with standard light microscopy, and fills a gap between cell and organism resolution. It spans from advanced fluorescence imaging of micrometric cell clusters to centimetre-size complete organisms. However, with larger volume specimens, new problems arise. Imaging deeper into tissues at high resolution poses challenges ranging from optical distortions to shadowing from opaque structures. This manuscript discusses the latest developments in mesoscale imaging and highlights limitations, namely labelling, clearing, absorption, scattering, and also sample handling. We then focus on approaches that seek to turn mesoscale imaging into a more quantitative technique, analogous to quantitative tomography in medical imaging, highlighting a future role for digital and physical phantoms as well as artificial intelligence.
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Affiliation(s)
- Sebastian Munck
- VIB‐KU Leuven Center for Brain & Disease ResearchLight Microscopy Expertise Unit & VIB BioImaging CoreLeuvenBelgium
- KU Leuven Department of NeurosciencesLeuven Brain InstituteLeuvenBelgium
| | | | - Abril Escamilla‐Ayala
- VIB‐KU Leuven Center for Brain & Disease ResearchLight Microscopy Expertise Unit & VIB BioImaging CoreLeuvenBelgium
- KU Leuven Department of NeurosciencesLeuven Brain InstituteLeuvenBelgium
| | - Axelle Kerstens
- VIB‐KU Leuven Center for Brain & Disease ResearchLight Microscopy Expertise Unit & VIB BioImaging CoreLeuvenBelgium
- KU Leuven Department of NeurosciencesLeuven Brain InstituteLeuvenBelgium
| | - Sergio Gabarre
- VIB‐KU Leuven Center for Brain & Disease ResearchLight Microscopy Expertise Unit & VIB BioImaging CoreLeuvenBelgium
- KU Leuven Department of NeurosciencesLeuven Brain InstituteLeuvenBelgium
| | | | | | - Rebecca Craig
- Department of Physics, SUPAUniversity of StrathclydeGlasgowUK
| | - Emmanuel G. Reynaud
- School of Biomolecular and Biomedical ScienceUniversity College DublinDublinBelfieldIreland
| | - Jim Swoger
- European Molecular Biology Laboratory (EMBL) BarcelonaBarcelonaSpain
| | - Gail McConnell
- Department of Physics, SUPAUniversity of StrathclydeGlasgowUK
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Minelli A, Valero-Gracia A. Spatially and Temporally Distributed Complexity-A Refreshed Framework for the Study of GRN Evolution. Cells 2022; 11:cells11111790. [PMID: 35681485 PMCID: PMC9179533 DOI: 10.3390/cells11111790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 05/24/2022] [Accepted: 05/28/2022] [Indexed: 11/16/2022] Open
Abstract
Irrespective of the heuristic value of interpretations of developmental processes in terms of gene regulatory networks (GRNs), larger-angle views often suffer from: (i) an inadequate understanding of the relationship between genotype and phenotype; (ii) a predominantly zoocentric vision; and (iii) overconfidence in a putatively hierarchical organization of animal body plans. Here, we constructively criticize these assumptions. First, developmental biology is pervaded by adultocentrism, but development is not necessarily egg to adult. Second, during development, many unicells undergo transcriptomic profile transitions that are comparable to those recorded in pluricellular organisms; thus, their study should not be neglected from the GRN perspective. Third, the putatively hierarchical nature of the animal body is mirrored in the GRN logic, but in relating genotype to phenotype, independent assessments of the dynamics of the regulatory machinery and the animal’s architecture are required, better served by a combinatorial than by a hierarchical approach. The trade-offs between spatial and temporal aspects of regulation, as well as their evolutionary consequences, are also discussed. Multicellularity may derive from a unicell’s sequential phenotypes turned into different but coexisting, spatially arranged cell types. In turn, polyphenism may have been a crucial mechanism involved in the origin of complex life cycles.
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Affiliation(s)
- Alessandro Minelli
- Department of Biology, University of Padova, Via U. Bassi 58B, 35132 Padova, Italy
- Correspondence:
| | - Alberto Valero-Gracia
- Natural History Museum, University of Oslo, Blindern, P.O. Box 1172, 0318 Oslo, Norway;
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Bobes RJ, Estrada K, Rios-Valencia DG, Calderón-Gallegos A, de la Torre P, Carrero JC, Sanchez-Flores A, Laclette JP. The Genomes of Two Strains of Taenia crassiceps the Animal Model for the Study of Human Cysticercosis. Front Cell Infect Microbiol 2022; 12:876839. [PMID: 35619649 PMCID: PMC9128525 DOI: 10.3389/fcimb.2022.876839] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 04/12/2022] [Indexed: 12/13/2022] Open
Abstract
Human cysticercosis by Taenia solium is the major cause of neurological illness in countries of Africa, Southeast Asia, and the Americas. Publication of four cestode genomes (T. solium, Echinococcus multilocularis, E. granulosus and Hymenolepis microstoma) in the last decade, marked the advent of novel approaches on the study of the host-parasite molecular crosstalk for cestode parasites of importance for human and animal health. Taenia crassiceps is another cestode parasite, closely related to T. solium, which has been used in numerous studies as an animal model for human cysticercosis. Therefore, characterization of the T. crassiceps genome will also contribute to the understanding of the human infection. Here, we report the genome of T. crassiceps WFU strain, reconstructed to a noncontiguous finished resolution and performed a genomic and differential expression comparison analysis against ORF strain. Both strain genomes were sequenced using Oxford Nanopore (MinION) and Illumina technologies, achieving high quality assemblies of about 107 Mb for both strains. Dotplot comparison between WFU and ORF demonstrated that both genomes were extremely similar. Additionally, karyotyping results for both strains failed to demonstrate a difference in chromosome composition. Therefore, our results strongly support the concept that the absence of scolex in the ORF strain of T. crassiceps was not the result of a chromosomal loss as proposed elsewhere. Instead, it appears to be the result of subtle and extensive differences in the regulation of gene expression. Analysis of variants between the two strains identified 2,487 sites with changes distributed in 31 of 65 scaffolds. The differential expression analysis revealed that genes related to development and morphogenesis in the ORF strain might be involved in the lack of scolex formation.
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Affiliation(s)
- Raúl J. Bobes
- Biomedical Research Institute, Universidad Nacional Autónoma de México, CDMX, Mexico
| | - Karel Estrada
- Biotechnology Institute, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | | | | | - Patricia de la Torre
- Biomedical Research Institute, Universidad Nacional Autónoma de México, CDMX, Mexico
| | - Julio C. Carrero
- Biomedical Research Institute, Universidad Nacional Autónoma de México, CDMX, Mexico
| | - Alejandro Sanchez-Flores
- Biotechnology Institute, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
- *Correspondence: Juan P. Laclette, ; Alejandro Sanchez-Flores,
| | - Juan P. Laclette
- Biomedical Research Institute, Universidad Nacional Autónoma de México, CDMX, Mexico
- *Correspondence: Juan P. Laclette, ; Alejandro Sanchez-Flores,
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11
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Ludueña RF. Possible Roles of Specific Amino Acids in β-Tubulin Isotypes in the Growth and Maintenance of Neurons: Novel Insights From Cephalopod Mollusks. Front Mol Neurosci 2022; 15:838393. [PMID: 35493322 PMCID: PMC9048481 DOI: 10.3389/fnmol.2022.838393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 02/17/2022] [Indexed: 11/18/2022] Open
Abstract
Microtubules, are formed of the protein tubulin, which is a heterodimer of α- and β-tubulin subunits. Both α- and β-tubulin exist as numerous isotypes, differing in amino acid sequence and tissue distribution. Among the vertebrate β isotypes, βIII has a very narrow distribution, being found primarily in neurons and in advanced cancers. The places in the amino acid sequence where βIII differs from the other β isotypes are highly conserved in evolution. βIII appears to be highly resistant to reactive oxygen species and it forms highly dynamic microtubules. The first property would be very useful in neurons, which have high concentrations of free radicals, and the high dynamicity would aid neurite outgrowth. The same properties make βIII useful in cancers. Examination of the amino acid sequences indicates a cysteine cluster at positions 124–129 in βIII (CXXCXC). This occurs in all βIII isotypes but not in βI, βII, or βIV. βIII also lacks the easily oxidized C239. Both features could play roles in free radical resistance. Many aggressive tumors over-express βIII. However, a recent study of breast cancer patients showed that many of them mutated their βI, βII, and βIV at particular places to change the residues to those found at the corresponding sites in βIII; these are all sites that are highly conserved in vertebrate βIII. It is possible that these residues are important, not only in the resistance to free radicals, but also in the high dynamicity of βIII. The cephalopod mollusks are well known to be highly intelligent and can remodel their own brains. Interestingly, several cephalopods contain the cysteine cluster as well as up to 7 of the 17 residues that are highly conserved in vertebrate βIII, but are not found in βI, βII, or βIV. In short, it is possible that we are looking at a case of convergent evolution, that a βIII-like isotype may be required for neuronal growth and function and that a structure-function study of the particular residues conserved between vertebrate βIII and cephalopod tubulin isotypes could greatly increase our understanding of the role of the various tubulin isotypes in neuronal growth and function and could aid in the development of novel anti-tumor drugs.
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Dos Santos GB, da Silva ED, Kitano ES, Battistella ME, Monteiro KM, de Lima JC, Ferreira HB, Serrano SMDT, Zaha A. Proteomic profiling of hydatid fluid from pulmonary cystic echinococcosis. Parasit Vectors 2022; 15:99. [PMID: 35313982 PMCID: PMC8935821 DOI: 10.1186/s13071-022-05232-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 03/03/2022] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Most cystic echinococcosis cases in Southern Brazil are caused by Echinococcus granulosus and Echinococcus ortleppi. Proteomic studies of helminths have increased our knowledge about the molecular survival strategies that are used by parasites. Here, we surveyed the protein content of the hydatid fluid compartment in E. granulosus and E. ortleppi pulmonary bovine cysts to better describe and compare their molecular arsenal at the host-parasite interface. METHODS Hydatid fluid samples from three isolates of each species were analyzed using mass spectrometry-based proteomics (LC-MS/MS). In silico functional analyses of the identified proteins were performed to examine parasite survival strategies. RESULTS The identified hydatid fluid protein profiles showed a predominance of parasite proteins compared to host proteins that infiltrate the cysts. We identified 280 parasitic proteins from E. granulosus and 251 from E. ortleppi, including 52 parasitic proteins that were common to all hydatid fluid samples. The in silico functional analysis revealed important molecular functions and processes that are active in pulmonary cystic echinococcosis, such as adhesion, extracellular structures organization, development regulation, signaling transduction, and enzyme activity. CONCLUSIONS The protein profiles described here provide evidence of important mechanisms related to basic cellular processes and functions that act at the host-parasite interface in cystic echinococcosis. The molecular tools used by E. granulosus and E. ortleppi for survival within the host are potential targets for new therapeutic approaches to treat cystic echinococcosis and other larval cestodiases.
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Affiliation(s)
- Guilherme Brzoskowski Dos Santos
- Laboratório de Biologia Molecular de Cestódeos, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Edileuza Danieli da Silva
- Laboratório de Biologia Molecular de Cestódeos, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Eduardo Shigueo Kitano
- Laboratório de Toxinologia Aplicada, Center of Toxins, Immune-Response and Cell Signaling (CeTICS), Instituto Butantan, São Paulo, Brazil
| | - Maria Eduarda Battistella
- Laboratório de Biologia Molecular de Cestódeos, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Karina Mariante Monteiro
- Laboratório de Genômica Estrutural E Funcional, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Jeferson Camargo de Lima
- Laboratório de Genômica Estrutural E Funcional, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Henrique Bunselmeyer Ferreira
- Laboratório de Biologia Molecular de Cestódeos, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.,Laboratório de Genômica Estrutural E Funcional, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Solange Maria de Toledo Serrano
- Laboratório de Toxinologia Aplicada, Center of Toxins, Immune-Response and Cell Signaling (CeTICS), Instituto Butantan, São Paulo, Brazil
| | - Arnaldo Zaha
- Laboratório de Biologia Molecular de Cestódeos, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil. .,Laboratório de Genômica Estrutural E Funcional, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.
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13
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Kwak HJ, Lee SG, Park SC, Kim JH, Weisblat DA, Park C, Cho SJ. Head transcriptome profiling of glossiphoniid leech ( Helobdella austinensis) reveals clues about proboscis development. Open Biol 2022; 12:210298. [PMID: 35232253 PMCID: PMC8889196 DOI: 10.1098/rsob.210298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Cephalization refers to the evolutionary trend towards the concentration of neural tissues, sensory organs, mouth and associated structures at the front end of bilaterian animals. Comprehensive studies on gene expression related to the anterior formation in invertebrate models are currently lacking. In this study, we performed de novo transcriptional profiling on a proboscis-bearing leech (Helobdella austinensis) to identify differentially expressed genes (DEGs) in the anterior versus other parts of the body, in particular to find clues as to the development of the proboscis. Between the head and the body, 132 head-specific DEGs were identified, of which we chose 11 to investigate their developmental function during embryogenesis. Analysis of the spatial expression of these genes using in situ hybridization showed that they were characteristically expressed in the anterior region of the developing embryo, including the proboscis. Our results provide information on the genes related to head formation and insights into the function of proboscis-related genes during organogenesis with the potential roles of genes not yet characterized.
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Affiliation(s)
- Hee-Jin Kwak
- Department of Biological Sciences and Biotechnology, College of Natural Sciences, Chungbuk National University, Cheongju, Chungbuk 28644, Republic of Korea,Department of Ecology, Evolution and Behavior, Alexander Silberman Institute of Life Sciences, Faculty of Science, Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Sung-Gwon Lee
- School of Biological Sciences and Technology, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Soon Cheol Park
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Jung-Hyeuk Kim
- Wildlife Disease Response Team, National Institute of Wildlife Disease Control and Prevention, Incheon 22689, Republic of Korea
| | - David A. Weisblat
- Department of Molecular and Cell Biology, University of California, 385 Weill Hall, Berkeley, CA 94720-3200, USA
| | - Chungoo Park
- School of Biological Sciences and Technology, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Sung-Jin Cho
- Department of Biological Sciences and Biotechnology, College of Natural Sciences, Chungbuk National University, Cheongju, Chungbuk 28644, Republic of Korea
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14
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Tkach VV. Presidential Address: Parasitology and Technology: A Perfect Symbiosis. J Parasitol 2021. [DOI: 10.1645/21-115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Affiliation(s)
- Vasyl V. Tkach
- Biology Department, University of North Dakota, 10 Cornell Street, Stop 9019, Grand Forks, North Dakota 58202-9019
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15
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Mohammadi MA, Harandi MF, McManus DP, Mansouri M. Genome-wide transcriptome analysis of the early developmental stages of Echinococcus granulosus protoscoleces reveals extensive alternative splicing events in the spliceosome pathway. Parasit Vectors 2021; 14:574. [PMID: 34772444 PMCID: PMC8587495 DOI: 10.1186/s13071-021-05067-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 10/15/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The complex life cycle of Echinococcus granulosus involves numerous environmental conditions within different intermediate and definitive hosts. This requires adaptation at different levels of transcript regulation. Alternative splicing (AS) and the related cellular functions as one of the major fields of post-genomics has been poorly studied in tapeworms. In the present study, we investigated AS events and their potential biological effects in E. granulosus. METHODS Whole transcriptome sequencing data of four groups of protoscoleces were prepared for RNA-seq library construction. Fresh protoscoleces were either used as non-induced controls (NT group) or incubated for 15 min with pepsin (PEP group) and cultivated in a biphasic medium for 12 and 24 h (12 and 24 h groups). The frequency and different types of AS events were identified using rMATS software. Functional annotations and gene ontology of differential AS (DAS) genes were performed using Blast2GO software. AS events were experimentally validated by PCR on the protoscolex cDNAs using specific primers for each gene. RESULTS At least one AS event was found in 38.1% of the genes (3904 out of 10,245) in the protoscoleces during early strobilar development. The genes were associated primarily with cellular and metabolic processes and binding and catalytic activity. KEGG pathway analysis of DAS events revealed a number of genes belonging to different components of the spliceosome complex. These genes tended to belong to common SR proteins, U1-related factors, U2-related factors, complex A-specific factors and other splicing-related proteins. CONCLUSIONS The high number of AS events in the transcriptome regulatory mechanisms indicates the essential rapid molecular processes required by the parasite for adaptation in different environments.
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Affiliation(s)
- Mohammad Ali Mohammadi
- Student Research Committee, Afzalipour School of Medicine, Kerman University of Medical Sciences, Kerman, Iran
- Research Center for Hydatid Disease in Iran, Afzalipour School of Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Majid Fasihi Harandi
- Research Center for Hydatid Disease in Iran, Afzalipour School of Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Donald P. McManus
- Molecular Parasitology Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, QLD Australia
| | - Mehdi Mansouri
- Department of Agricultural Biotechnology, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran
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Kamenetzky L, Maldonado LL, Cucher MA. Cestodes in the genomic era. Parasitol Res 2021; 121:1077-1089. [PMID: 34665308 DOI: 10.1007/s00436-021-07346-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 10/10/2021] [Indexed: 12/20/2022]
Abstract
The first cestode genomes were obtained by an international consortium led by the Wellcome Sanger Institute that included representative institutions from countries where the sequenced parasites have been studied for decades, in part because they are etiological agents of endemic diseases (Argentina, Uruguay, Mexico, Canada, UK, Germany, Switzerland, Ireland, USA, Japan, and China). After this, several complete genomes were obtained reaching 16 species to date. Cestode genomes have smaller relative size compared to other animals including free-living flatworms. Moreover, the features genome size and repeat content seem to differ in the two analyzed orders. Cyclophyllidean species have smaller genomes and with fewer repetitive content than Diphyllobothriidean species. On average, cestode genomes have 13,753 genes with 6 exons per gene and 41% GC content. More than 5,000 shared cestode proteins were accurately annotated by the integration of gene predictions and transcriptome evidence being more than 40% of these proteins of unknown function. Several gene losses and reduction of gene families were found and could be related to the extreme parasitic lifestyle of these species. The application of cutting-edge sequencing technology allowed the characterization of the terminal sequences of chromosomes that possess unique characteristics. Here, we review the current status of knowledge of complete cestode genomes and place it within a comparative genomics perspective. Multidisciplinary work together with the implementation of new technologies will provide valuable information that can certainly improve our chances to finally eradicate or at least control diseases caused by cestodes.
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Affiliation(s)
- Laura Kamenetzky
- iB3, Instituto de Biociencias, Departamento de Fisiología Y Biología Molecular Y Celular, Facultad de Ciencias Exactas Y Naturales, Universidad de Buenos Aires, Biotecnología y Biología traslacional, Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina.
| | - Lucas L Maldonado
- Department of Microbiology, School of Medicine, University of Buenos Aires, Buenos Aires, Argentina.,Institute of Research On Microbiology and Medical Parasitology (IMPaM, UBA-CONICET), University of Buenos Aires, Buenos Aires, Argentina
| | - Marcela A Cucher
- Department of Microbiology, School of Medicine, University of Buenos Aires, Buenos Aires, Argentina.,Institute of Research On Microbiology and Medical Parasitology (IMPaM, UBA-CONICET), University of Buenos Aires, Buenos Aires, Argentina
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Wititkornkul B, Hulme BJ, Tomes JJ, Allen NR, Davis CN, Davey SD, Cookson AR, Phillips HC, Hegarty MJ, Swain MT, Brophy PM, Wonfor RE, Morphew RM. Evidence of Immune Modulators in the Secretome of the Equine Tapeworm Anoplocephala perfoliata. Pathogens 2021; 10:pathogens10070912. [PMID: 34358062 PMCID: PMC8308605 DOI: 10.3390/pathogens10070912] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 07/14/2021] [Accepted: 07/15/2021] [Indexed: 12/15/2022] Open
Abstract
Anoplocephala perfoliata is a neglected gastro-intestinal tapeworm, commonly infecting horses worldwide. Molecular investigation of A. perfoliata is hampered by a lack of tools to better understand the host-parasite interface. This interface is likely influenced by parasite derived immune modulators released in the secretome as free proteins or components of extracellular vesicles (EVs). Therefore, adult RNA was sequenced and de novo assembled to generate the first A. perfoliata transcriptome. In addition, excretory secretory products (ESP) from adult A. perfoliata were collected and EVs isolated using size exclusion chromatography, prior to proteomic analysis of the EVs, the EV surface and EV depleted ESP. Transcriptome analysis revealed 454 sequences homologous to known helminth immune modulators including two novel Sigma class GSTs, five α-HSP90s, and three α-enolases with isoforms of all three observed within the proteomic analysis of the secretome. Furthermore, secretome proteomics identified common helminth proteins across each sample with known EV markers, such as annexins and tetraspanins, observed in EV fractions. Importantly, 49 of the 454 putative immune modulators were identified across the secretome proteomics contained within and on the surface of EVs in addition to those identified in free ESP. This work provides the molecular tools for A. perfoliata to reveal key players in the host-parasite interaction within the horse host.
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Affiliation(s)
- Boontarikaan Wititkornkul
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth SY23 3DA, UK; (B.W.); (B.J.H.); (J.J.T.); (N.R.A.); (C.N.D.); (S.D.D.); (A.R.C.); (H.C.P.); (M.J.H.); (M.T.S.); (P.M.B.)
- Faculty of Veterinary Science, Rajamangala University of Technology Srivijaya, Nakhon Si Thammarat 80240, Thailand
| | - Benjamin J. Hulme
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth SY23 3DA, UK; (B.W.); (B.J.H.); (J.J.T.); (N.R.A.); (C.N.D.); (S.D.D.); (A.R.C.); (H.C.P.); (M.J.H.); (M.T.S.); (P.M.B.)
| | - John J. Tomes
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth SY23 3DA, UK; (B.W.); (B.J.H.); (J.J.T.); (N.R.A.); (C.N.D.); (S.D.D.); (A.R.C.); (H.C.P.); (M.J.H.); (M.T.S.); (P.M.B.)
| | - Nathan R. Allen
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth SY23 3DA, UK; (B.W.); (B.J.H.); (J.J.T.); (N.R.A.); (C.N.D.); (S.D.D.); (A.R.C.); (H.C.P.); (M.J.H.); (M.T.S.); (P.M.B.)
| | - Chelsea N. Davis
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth SY23 3DA, UK; (B.W.); (B.J.H.); (J.J.T.); (N.R.A.); (C.N.D.); (S.D.D.); (A.R.C.); (H.C.P.); (M.J.H.); (M.T.S.); (P.M.B.)
| | - Sarah D. Davey
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth SY23 3DA, UK; (B.W.); (B.J.H.); (J.J.T.); (N.R.A.); (C.N.D.); (S.D.D.); (A.R.C.); (H.C.P.); (M.J.H.); (M.T.S.); (P.M.B.)
| | - Alan R. Cookson
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth SY23 3DA, UK; (B.W.); (B.J.H.); (J.J.T.); (N.R.A.); (C.N.D.); (S.D.D.); (A.R.C.); (H.C.P.); (M.J.H.); (M.T.S.); (P.M.B.)
| | - Helen C. Phillips
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth SY23 3DA, UK; (B.W.); (B.J.H.); (J.J.T.); (N.R.A.); (C.N.D.); (S.D.D.); (A.R.C.); (H.C.P.); (M.J.H.); (M.T.S.); (P.M.B.)
| | - Matthew J. Hegarty
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth SY23 3DA, UK; (B.W.); (B.J.H.); (J.J.T.); (N.R.A.); (C.N.D.); (S.D.D.); (A.R.C.); (H.C.P.); (M.J.H.); (M.T.S.); (P.M.B.)
| | - Martin T. Swain
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth SY23 3DA, UK; (B.W.); (B.J.H.); (J.J.T.); (N.R.A.); (C.N.D.); (S.D.D.); (A.R.C.); (H.C.P.); (M.J.H.); (M.T.S.); (P.M.B.)
| | - Peter M. Brophy
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth SY23 3DA, UK; (B.W.); (B.J.H.); (J.J.T.); (N.R.A.); (C.N.D.); (S.D.D.); (A.R.C.); (H.C.P.); (M.J.H.); (M.T.S.); (P.M.B.)
| | - Ruth E. Wonfor
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth SY23 3DA, UK; (B.W.); (B.J.H.); (J.J.T.); (N.R.A.); (C.N.D.); (S.D.D.); (A.R.C.); (H.C.P.); (M.J.H.); (M.T.S.); (P.M.B.)
- Correspondence: (R.E.W.); (R.M.M.)
| | - Russell M. Morphew
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth SY23 3DA, UK; (B.W.); (B.J.H.); (J.J.T.); (N.R.A.); (C.N.D.); (S.D.D.); (A.R.C.); (H.C.P.); (M.J.H.); (M.T.S.); (P.M.B.)
- Correspondence: (R.E.W.); (R.M.M.)
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Genome of the fatal tapeworm Sparganum proliferum uncovers mechanisms for cryptic life cycle and aberrant larval proliferation. Commun Biol 2021; 4:649. [PMID: 34059788 PMCID: PMC8166898 DOI: 10.1038/s42003-021-02160-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 04/29/2021] [Indexed: 12/13/2022] Open
Abstract
The cryptic parasite Sparganum proliferum proliferates in humans and invades tissues and organs. Only scattered cases have been reported, but S. proliferum infection is always fatal. However, S. proliferum’s phylogeny and life cycle remain enigmatic. To investigate the phylogenetic relationships between S. proliferum and other cestode species, and to examine the mechanisms underlying pathogenicity, we sequenced the entire genomes of S. proliferum and a closely related non–life-threatening tapeworm Spirometra erinaceieuropaei. Additionally, we performed larvae transcriptome analyses of S. proliferum plerocercoid to identify genes involved in asexual reproduction in the host. The genome sequences confirmed that the S. proliferum has experienced a clearly distinct evolutionary history from S. erinaceieuropaei. Moreover, we found that nonordinal extracellular matrix coordination allows asexual reproduction in the host, and loss of sexual maturity in S. proliferum are responsible for its fatal pathogenicity to humans. Our high-quality reference genome sequences should be valuable for future studies of pseudophyllidean tapeworm biology and parasitism. Kikuchi et al. sequence the genome of the fatal tapeworm Sparganum proliferum and a closely related non–life-threatening tapeworm Spirometra erinaceieuropaei, and describe its genomic features suggesting the natural history and molecular mechanisms underlying pathogenicity. Their findings indicate that nonordinal extracellular matrix coordination is important for its asexual reproduction, and suggest that loss of sexual maturity contributes to the fatal pathogenicity of S. proliferum to humans.
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Preza M, Calvelo J, Langleib M, Hoffmann F, Castillo E, Koziol U, Iriarte A. Stage-specific transcriptomic analysis of the model cestode Hymenolepis microstoma. Genomics 2021; 113:620-632. [PMID: 33485950 DOI: 10.1016/j.ygeno.2021.01.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 12/20/2020] [Accepted: 01/17/2021] [Indexed: 12/11/2022]
Abstract
Most parasitic flatworms go through different life stages with important physiological and morphological changes. In this work, we used a transcriptomic approach to analyze the main life-stages of the model tapeworm Hymenolepis microstoma (eggs, cysticercoids, and adults). Our results showed massive transcriptomic changes in this life cycle, including key gene families that contribute substantially to the expression load in each stage. In particular, different members of the cestode-specific hydrophobic ligand-binding protein (HLBP) family are among the most highly expressed genes in each life stage. We also found the transcriptomic signature of major metabolic changes during the transition from cysticercoids to adult worms. Thus, this work contributes to uncovering the gene expression changes that accompany the development of this important cestode model species, and to the best of our knowledge represents the first transcriptomic study with robust replicates spanning all of the main life stages of a tapeworm.
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Affiliation(s)
- Matías Preza
- Sección Biología Celular, Facultad de Ciencias, Universidad de la República, Montevideo 11400, Uruguay
| | - Javier Calvelo
- Sección Biología Celular, Facultad de Ciencias, Universidad de la República, Montevideo 11400, Uruguay; Laboratorio Biología Computacional, Departamento de Desarrollo Biotecnológico, Instituto de Higiene, Facultad de Medicina, Universidad de la República, Montevideo 11600, Uruguay
| | - Mauricio Langleib
- Laboratorio Biología Computacional, Departamento de Desarrollo Biotecnológico, Instituto de Higiene, Facultad de Medicina, Universidad de la República, Montevideo 11600, Uruguay
| | - Federico Hoffmann
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, MS 39762, United States
| | - Estela Castillo
- Sección Bioquímica, Facultad de Ciencias, Universidad de la República, Montevideo 11400, Uruguay
| | - Uriel Koziol
- Sección Biología Celular, Facultad de Ciencias, Universidad de la República, Montevideo 11400, Uruguay.
| | - Andrés Iriarte
- Laboratorio Biología Computacional, Departamento de Desarrollo Biotecnológico, Instituto de Higiene, Facultad de Medicina, Universidad de la República, Montevideo 11600, Uruguay.
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Olson PD, Tracey A, Baillie A, James K, Doyle SR, Buddenborg SK, Rodgers FH, Holroyd N, Berriman M. Complete representation of a tapeworm genome reveals chromosomes capped by centromeres, necessitating a dual role in segregation and protection. BMC Biol 2020; 18:165. [PMID: 33167983 PMCID: PMC7653826 DOI: 10.1186/s12915-020-00899-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 10/14/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Chromosome-level assemblies are indispensable for accurate gene prediction, synteny assessment, and understanding higher-order genome architecture. Reference and draft genomes of key helminth species have been published, but little is yet known about the biology of their chromosomes. Here, we present the complete genome of the tapeworm Hymenolepis microstoma, providing a reference quality, end-to-end assembly that represents the first fully assembled genome of a spiralian/lophotrochozoan, revealing new insights into chromosome evolution. RESULTS Long-read sequencing and optical mapping data were added to previous short-read data enabling complete re-assembly into six chromosomes, consistent with karyology. Small genome size (169 Mb) and lack of haploid variation (1 SNP/3.2 Mb) contributed to exceptionally high contiguity with only 85 gaps remaining in regions of low complexity sequence. Resolution of repeat regions reveals novel gene expansions, micro-exon genes, and spliced leader trans-splicing, and illuminates the landscape of transposable elements, explaining observed length differences in sister chromatids. Syntenic comparison with other parasitic flatworms shows conserved ancestral linkage groups indicating that the H. microstoma karyotype evolved through fusion events. Strikingly, the assembly reveals that the chromosomes terminate in centromeric arrays, indicating that these motifs play a role not only in segregation, but also in protecting the linear integrity and full lengths of chromosomes. CONCLUSIONS Despite strong conservation of canonical telomeres, our results show that they can be substituted by more complex, species-specific sequences, as represented by centromeres. The assembly provides a robust platform for investigations that require complete genome representation.
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Affiliation(s)
- Peter D. Olson
- Department of Life Sciences, Natural History Museum, Cromwell Road, London, SW7 5BD UK
| | - Alan Tracey
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA UK
| | - Andrew Baillie
- Department of Life Sciences, Natural History Museum, Cromwell Road, London, SW7 5BD UK
| | - Katherine James
- Department of Life Sciences, Natural History Museum, Cromwell Road, London, SW7 5BD UK
- Department of Applied Sciences, Northumbria University, Newcastle upon Tyne, NE1 8ST UK
| | - Stephen R. Doyle
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA UK
| | - Sarah K. Buddenborg
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA UK
| | - Faye H. Rodgers
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA UK
| | - Nancy Holroyd
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA UK
| | - Matt Berriman
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA UK
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21
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Camargo de Lima J, Floriani MA, Debarba JA, Paludo GP, Monteiro KM, Moura H, Barr JR, Zaha A, Ferreira HB. Dynamics of protein synthesis in the initial steps of strobilation in the model cestode parasite Mesocestoides corti (syn. vogae). J Proteomics 2020; 228:103939. [PMID: 32798775 PMCID: PMC10491476 DOI: 10.1016/j.jprot.2020.103939] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 08/05/2020] [Accepted: 08/10/2020] [Indexed: 01/24/2023]
Abstract
Mesocestoides corti (syn. vogae) is a useful model for developmental studies of platyhelminth parasites of the Cestoda class, such as Taenia spp. or Echinococcus spp. It has been used in studies to characterize cestode strobilation, i.e. the development of larvae into adult worms. So far, little is known about the initial molecular events involved in cestode strobilation and, therefore, we carried out a study to characterize newly synthesized (NS) proteins upon strobilation induction. An approach based on bioorthogonal noncanonical amino acid tagging and mass spectrometry was used to label, isolate, identify, and quantify NS proteins in the initial steps of M. corti strobilation. Overall, 121 NS proteins were detected exclusively after induction of strobilation, including proteins related to development pathways, such as insulin and notch signaling. Metabolic changes that take place in the transition from the larval stage to adult worm were noted in special NS protein subsets related to developmental processes, such as focal adhesion, cell leading edge, and maintenance of location. The data shed light on mechanisms underlying early steps of cestode strobilation and enabled identification of possible developmental markers. We also consider the use of developmental responsive proteins as potential drug targets for developing novel anthelmintics. BIOLOGICAL SIGNIFICANCE: Larval cestodiases are life-threatening parasitic diseases that affect both man and domestic animals worldwide. Cestode parasites present complex life cycles, in which they undergo major morphological and physiological changes in the transition from one life-stage to the next. One of these transitions occurs during cestode strobilation, when the mostly undifferentiated and non-segmented larval or pre-adult form develops into a fully segmented and sexually differentiated (strobilated) adult worm. Although the proteomes of bona fide larvae and strobialted adults have been previously characterized for a few cestode species, little is still known about the dynamic of protein synthesis during the early steps of cestode strobilation. Now, the assessment of newly synthesized (NS) proteins within the first 48 h of strobilation the model cestode M. corti allowed to shed light on molecular mechanisms that are triggered by strobilation induction. The functional analyses of this repertoire of over a hundred NS proteins pointed out to changes in metabolism and activation of classical developmental signaling pathways in early strobilation. Many of the identified NS proteins may become valuable cestode developmental markers and their involvement in vital processes make them also good candidate targets for novel anthelmintic drugs.
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Affiliation(s)
- Jeferson Camargo de Lima
- Programa de Pós-Graduação em Biologia Molecular e Celular, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul (UFRGS), Brazil; Laboratório de Genômica Estrutural e Funcional, Centro de Biotecnologia, UFRGS, Porto Alegre, RS, Brazil
| | - Maiara Anschau Floriani
- Laboratório de Genômica Estrutural e Funcional, Centro de Biotecnologia, UFRGS, Porto Alegre, RS, Brazil
| | - João Antônio Debarba
- Programa de Pós-Graduação em Biologia Molecular e Celular, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul (UFRGS), Brazil; Laboratório de Biologia Molecular de Cestódeos, Centro de Biotecnologia, UFRGS, Porto Alegre, RS, Brazil
| | - Gabriela Prado Paludo
- Programa de Pós-Graduação em Biologia Molecular e Celular, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul (UFRGS), Brazil; Laboratório de Genômica Estrutural e Funcional, Centro de Biotecnologia, UFRGS, Porto Alegre, RS, Brazil
| | - Karina Mariante Monteiro
- Programa de Pós-Graduação em Biologia Molecular e Celular, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul (UFRGS), Brazil; Laboratório de Genômica Estrutural e Funcional, Centro de Biotecnologia, UFRGS, Porto Alegre, RS, Brazil; Laboratório de Biologia Molecular de Cestódeos, Centro de Biotecnologia, UFRGS, Porto Alegre, RS, Brazil
| | - Hercules Moura
- Biological Mass Spectrometry Laboratory, Clinical Chemistry Branch, Division of Laboratory Sciences, National Center for Environmental Health, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | - John R Barr
- Biological Mass Spectrometry Laboratory, Clinical Chemistry Branch, Division of Laboratory Sciences, National Center for Environmental Health, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | - Arnaldo Zaha
- Programa de Pós-Graduação em Biologia Molecular e Celular, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul (UFRGS), Brazil; Laboratório de Biologia Molecular de Cestódeos, Centro de Biotecnologia, UFRGS, Porto Alegre, RS, Brazil
| | - Henrique Bunselmeyer Ferreira
- Programa de Pós-Graduação em Biologia Molecular e Celular, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul (UFRGS), Brazil; Laboratório de Genômica Estrutural e Funcional, Centro de Biotecnologia, UFRGS, Porto Alegre, RS, Brazil; Laboratório de Biologia Molecular de Cestódeos, Centro de Biotecnologia, UFRGS, Porto Alegre, RS, Brazil.
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22
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James K, Olson PD. The tapeworm interactome: inferring confidence scored protein-protein interactions from the proteome of Hymenolepis microstoma. BMC Genomics 2020; 21:346. [PMID: 32380953 PMCID: PMC7204028 DOI: 10.1186/s12864-020-6710-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 03/30/2020] [Indexed: 12/14/2022] Open
Abstract
Background Reference genome and transcriptome assemblies of helminths have reached a level of completion whereby secondary analyses that rely on accurate gene estimation or syntenic relationships can be now conducted with a high level of confidence. Recent public release of the v.3 assembly of the mouse bile-duct tapeworm, Hymenolepis microstoma, provides chromosome-level characterisation of the genome and a stabilised set of protein coding gene models underpinned by bioinformatic and empirical data. However, interactome data have not been produced. Conserved protein-protein interactions in other organisms, termed interologs, can be used to transfer interactions between species, allowing systems-level analysis in non-model organisms. Results Here, we describe a probabilistic, integrated network of interologs for the H. microstoma proteome, based on conserved protein interactions found in eukaryote model species. Almost a third of the 10,139 gene models in the v.3 assembly could be assigned interaction data and assessment of the resulting network indicates that topologically-important proteins are related to essential cellular pathways, and that the network clusters into biologically meaningful components. Moreover, network parameters are similar to those of single-species interaction networks that we constructed in the same way for S. cerevisiae, C. elegans and H. sapiens, demonstrating that information-rich, system-level analyses can be conducted even on species separated by a large phylogenetic distance from the major model organisms from which most protein interaction evidence is based. Using the interolog network, we then focused on sub-networks of interactions assigned to discrete suites of genes of interest, including signalling components and transcription factors, germline multipotency genes, and genes differentially-expressed between larval and adult worms. Results show not only an expected bias toward highly-conserved proteins, such as components of intracellular signal transduction, but in some cases predicted interactions with transcription factors that aid in identifying their target genes. Conclusions With key helminth genomes now complete, systems-level analyses can provide an important predictive framework to guide basic and applied research on helminths and will become increasingly informative as new protein-protein interaction data accumulate.
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Affiliation(s)
- Katherine James
- Department of Applied Sciences, Northumbria University, Newcastle Upon Tyne, UK. .,Department of Life Sciences, The Natural History Museum, Cromwell Road, London, UK.
| | - Peter D Olson
- Department of Life Sciences, The Natural History Museum, Cromwell Road, London, UK
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Ito A, Li T, Wandra T, Dekumyoy P, Yanagida T, Okamoto M, Budke CM. Taeniasis and cysticercosis in Asia: A review with emphasis on molecular approaches and local lifestyles. Acta Trop 2019; 198:105075. [PMID: 31295430 DOI: 10.1016/j.actatropica.2019.105075] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 05/14/2019] [Accepted: 07/05/2019] [Indexed: 02/07/2023]
Abstract
Taeniasis is an important parasitic condition in Asia, especially since all three human-infecting Taenia spp., Taenia solium, Taenia saginata, and Taenia asiatica are found in this region. These three species are believed to be sympatrically distributed, with the largest disease burden found in remote and rural areas where people raise pigs and cattle in a traditional manner. Recent studies revealed that T. asiatica and T. saginata are genetically-related sister species that are not completely reproductively isolated from each other. Current evidence indicates that most T. asiatica adult worms are hybrid-derived descendants. Moving forward, nuclear DNA analysis will be critical in further assessing the species circulating locally. Lifestyle choices, such as the consumption of undercooked meat, are important in maintaining the life cycles of these parasites. In addition, poor hygiene and sanitation, in highly endemic areas, make disease control difficult, resulting in the need for sustainable education programs. An overview of the present situation of taeniasis and cysticercosis in Asia is provided, followed by a discussion of molecular approaches to species assessment and the impact of human lifestyles on parasite transmission.
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Affiliation(s)
- Akira Ito
- Department of Parasitology and Laboratory of NTDs, Asahikawa Medical University, Asahikawa, Japan.
| | - Tiaoying Li
- Institute of Parasitic Diseases, Sichuan Centers for Disease Control and Prevention, Chengdu, People's Republic of China
| | - Toni Wandra
- Directorate of Postgraduate, Sari Mutiara Indonesia University, Medan, Indonesia
| | - Paron Dekumyoy
- Department of Helminthology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Tetsuya Yanagida
- Laboratory of Veterinary Parasitology, Joint Faculty of Veterinary Medicine, Yamaguchi University, Yamaguchi, Japan
| | - Munehiro Okamoto
- Center for Human Evolution Modeling Research, Primate Research Institute, Kyoto University, Inuyama, Japan
| | - Christine M Budke
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine & Biomedical Sciences, Texas A & M University, College Station, Texas, USA
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24
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Rozario T, Quinn EB, Wang J, Davis RE, Newmark PA. Region-specific regulation of stem cell-driven regeneration in tapeworms. eLife 2019; 8:48958. [PMID: 31549962 PMCID: PMC6821492 DOI: 10.7554/elife.48958] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2019] [Accepted: 09/10/2019] [Indexed: 01/21/2023] Open
Abstract
Tapeworms grow at rates rivaling the fastest-growing metazoan tissues. To propagate they shed large parts of their body; to replace these lost tissues they regenerate proglottids (segments) as part of normal homeostasis. Their remarkable growth and regeneration are fueled by adult somatic stem cells that have yet to be characterized molecularly. Using the rat intestinal tapeworm, Hymenolepis diminuta, we find that regenerative potential is regionally limited to the neck, where head-dependent extrinsic signals create a permissive microenvironment for stem cell-driven regeneration. Using transcriptomic analyses and RNA interference, we characterize and functionally validate regulators of tapeworm growth and regeneration. We find no evidence that stem cells are restricted to the regeneration-competent neck. Instead, lethally irradiated tapeworms can be rescued when cells from either regeneration-competent or regeneration-incompetent regions are transplanted into the neck. Together, the head and neck tissues provide extrinsic cues that regulate stem cells, enabling region-specific regeneration in this parasite. Many worms have remarkable abilities to regrow and repair their bodies. The parasitic tapeworms, for example, can reach lengths of several meters and grow much more quickly than tissues in humans and other complex animals. This growth allows tapeworms to counteract the continual loss of the segments that make up their bodies, known as proglottids – a process that happens throughout their lives. The capacity to regenerate thousands of lost body segments and maintain an overall body length suggests that tapeworms have groups of stem cells in their body which can grow and divide to produce the new body parts. Yet, regeneration in tapeworms has not been closely studied. Rozario et al. have now examined Hymenolepsis diminuta, the rat tapeworm, and identified the neck of the tapeworm as crucial for its ability to regrow lost body segments. Further analysis identified two genes, zmym3 and pogzl, that are essential for cell division during tapeworm growth. However, Rozario et al. showed that these genes are active elsewhere in the worm’s body and that it is the conditions found specifically in the tapeworm’s neck that create the right environment for stem cells to enable regeneration of new segments. Tapeworms provide a valuable example for studying the growth of stem cells and these findings highlight the important role that the cells’ surroundings play in driving stem cell activity. These findings could also lead to new insights into how stem cells behave in other animals and could potentially lead to new approaches to prevent or treat tapeworm infections.
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Affiliation(s)
- Tania Rozario
- Morgridge Institute for Research, Madison, United States
| | - Edward B Quinn
- Morgridge Institute for Research, Madison, United States
| | - Jianbin Wang
- RNA Bioscience Initiative, Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, United States
| | - Richard E Davis
- RNA Bioscience Initiative, Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, United States
| | - Phillip A Newmark
- Morgridge Institute for Research, Madison, United States.,Howard Hughes Medical Institute, Chevy Chase, United States.,Department of Integrative Biology, University of Wisconsin-Madison, Madison, United States
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25
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Liu Y, Wang Z, Pang S, Zhao W, Kang L, Zhang Y, Zhang H, Yang J, Wang Z, Lu P, Xu M, Wang W, Bo X, Li Z. Evaluation of dynamic developmental processes and the molecular basis of the high body fat percentage of different proglottid types of Moniezia expansa. Parasit Vectors 2019; 12:390. [PMID: 31382993 PMCID: PMC6683355 DOI: 10.1186/s13071-019-3650-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 07/29/2019] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Moniezia expansa (Cyclophyllidea: Anoplocephalidae) is a large species of tapeworm that occurs in sheep and cattle and inhabits the small intestine, causing diarrhea and weight declines, leading to stockbreeding losses. Interestingly, the body fat percentage of M. expansa, which lacks the ability to synthesize fatty acids, is as high as 78% (dry weight) and all of the proglottids of M. expansa exhibit a dynamic developmental process from top to bottom. The aim of this paper is to identify the molecular basis of this high body fat percentage, the dynamic expression of developmental genes and their expression regulation patterns. RESULTS From 12 different proglottids (four sections: scolex and neck, immature, mature and gravid with three replicates), 13,874 transcripts and 680 differentially expressed genes (DEGs) were obtained. The gene expression patterns of the scolex and neck and immature proglottids were very similar, while those of the mature and gravid proglottids differed greatly. In addition, 13 lipid transport-related proteins were found in the DEGs, and the expression levels showed an increasing trend in the four proglottid types. Furthermore, it was shown that 33 homeobox genes, 9 of which were DEGs, had the highest expression in the scolex and neck section. The functional enrichment results of the DEGs were predominantly indicative of development-related processes, and there were also some signal transduction and metabolism results. The most striking result was the finding of Wnt signaling pathways, which appeared multiple times. Furthermore, the weighted gene co-expression networks were divided into 12 modules, of which the brown module was enriched with many development-related genes. CONCLUSIONS We hypothesize that M. expansa uses lipid transport-associated proteins to transport lipids from the host gut to obtain energy to facilitate its high fecundity. In addition, homeobox genes and Wnt signaling pathways play a core role in development and regeneration. The results promote research on the cell differentiation involved in the continuous growth and extension of body structures.
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Affiliation(s)
- Yi Liu
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production/Institute of Animal Husbandry and Veterinary, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
| | - Zhengrong Wang
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production/Institute of Animal Husbandry and Veterinary, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
| | - Shuai Pang
- Novogene Bioinformatics Institute, Beijing, China
| | - Wenjuan Zhao
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production/Institute of Animal Husbandry and Veterinary, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
| | - Lichao Kang
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production/Institute of Animal Husbandry and Veterinary, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
| | - Yanyan Zhang
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production/Institute of Animal Husbandry and Veterinary, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
| | - Hui Zhang
- Yangcheng Country Animal Husbandry and Veterinary Bureau, Jincheng, China
| | - Jingquan Yang
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production/Institute of Animal Husbandry and Veterinary, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
| | - Zhixin Wang
- Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Pingping Lu
- Xinjiang Tiankang Feed Technology Co., Ltd, Ürümqi, China
| | - Mengfei Xu
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production/Institute of Animal Husbandry and Veterinary, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
| | - Weiyi Wang
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production/Institute of Animal Husbandry and Veterinary, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
| | - Xinwen Bo
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production/Institute of Animal Husbandry and Veterinary, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China.
| | - Zhenzhen Li
- Novogene Bioinformatics Institute, Beijing, China.
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26
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Macchiaroli N, Cucher M, Kamenetzky L, Yones C, Bugnon L, Berriman M, Olson PD, Rosenzvit MC. Identification and expression profiling of microRNAs in Hymenolepis. Int J Parasitol 2019; 49:211-223. [PMID: 30677390 DOI: 10.1016/j.ijpara.2018.07.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 07/20/2018] [Accepted: 07/23/2018] [Indexed: 02/08/2023]
Abstract
Tapeworms (cestodes) of the genus Hymenolepis are the causative agents of hymenolepiasis, a neglected zoonotic disease. Hymenolepis nana is the most prevalent human tapeworm, especially affecting children. The genomes of Hymenolepis microstoma and H. nana have been recently sequenced and assembled. MicroRNAs (miRNAs), a class of small non-coding RNAs, are principle regulators of gene expression at the post-transcriptional level and are involved in many different biological processes. In previous work, we experimentally identified miRNA genes in the cestodes Echinococcus, Taenia and Mesocestoides. However, current knowledge about miRNAs in Hymenolepis is limited. In this work we described for the first known time the expression profile of the miRNA complement in H. microstoma, and discovered miRNAs in H. nana. We found a reduced complement of 37 evolutionarily conserved miRNAs, putatively reflecting their low morphological complexity and parasitic lifestyle. We found high expression of a few miRNAs in the larval stage of H. microstoma that are conserved in other cestodes, suggesting that these miRNAs may have important roles in development, survival and for host-parasite interplay. We performed a comparative analysis of the identified miRNAs across the Cestoda and showed that most of the miRNAs in Hymenolepis are located in intergenic regions, implying that they are independently transcribed. We found a Hymenolepis-specific cluster composed of three members of the mir-36 family. Also, we found that one of the neighboring genes of mir-10 was a Hox gene as in most bilaterial species. This study provides a valuable resource for further experimental research in cestode biology that might lead to improved detection and control of these neglected parasites. The comprehensive identification and expression analysis of Hymenolepis miRNAs can help to identify novel biomarkers for diagnosis and/or novel therapeutic targets for the control of hymenolepiasis.
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Affiliation(s)
- Natalia Macchiaroli
- Instituto de Investigaciones en Microbiología y Parasitología Médicas (IMPaM), Facultad de Medicina, Universidad de Buenos Aires (UBA)-Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Buenos Aires, Argentina
| | - Marcela Cucher
- Instituto de Investigaciones en Microbiología y Parasitología Médicas (IMPaM), Facultad de Medicina, Universidad de Buenos Aires (UBA)-Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Buenos Aires, Argentina
| | - Laura Kamenetzky
- Instituto de Investigaciones en Microbiología y Parasitología Médicas (IMPaM), Facultad de Medicina, Universidad de Buenos Aires (UBA)-Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Buenos Aires, Argentina
| | - Cristian Yones
- Research Institute for Signals, Systems and Computational Intelligence, (sinc(i)), FICH-UNL-Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Santa Fe, Argentina
| | - Leandro Bugnon
- Research Institute for Signals, Systems and Computational Intelligence, (sinc(i)), FICH-UNL-Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Santa Fe, Argentina
| | - Matt Berriman
- Parasite Genomics Group, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Peter D Olson
- Department of Life Sciences, The Natural History Museum, London, UK
| | - Mara Cecilia Rosenzvit
- Instituto de Investigaciones en Microbiología y Parasitología Médicas (IMPaM), Facultad de Medicina, Universidad de Buenos Aires (UBA)-Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Buenos Aires, Argentina.
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